Heat oven 300 degrees. Cook the bacon in a dutch oven over medium heat, stirring occasionally, until nearly crisp 5-7 mins. Add the onion, 1 tsp salt and 1/2 tsp pepper and cook, stirring occasionally,until the onion is soft, 4-6 mins more.
Add the beans, molasses,ketchup,mustard and 5 cups water to the pot and stir to combine;bring to a boil.
Cover the pot and transfer to oven. Bake until the liquid is reduced by half,about 2 1/2 hrs. Uncover and bake, stirring onve, until the cooking liquid is thickened, 1-1 1/4 hrs more. Stir in the vinegar and serve.
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